9FU0

CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb9FU0/pdb
EM Map EMD-50753: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Mycolicibacterium smegmatis
Expression System: Mycolicibacterium smegmatis
Mutation(s): No

Deposited: 2024-06-25 Released: 2024-11-20
Deposition Author(s): Kovalova, T., Krol, S., Gamiz-Hernandez, A., Sjostrand, D., Kaila, V., Brzezinski, P., Hogbom, M.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Inhibition mechanism of potential anti-tuberculosis compound lansoprazole sulfide

Kovalova, T., Krol, S., Gamiz-Hernandez, A., Sjostrand, D., Kaila, V., Brzezinski, P., Hogbom, M.

To be published.

Macromolecule Content

Total Structure Weight: 521.81 kDa
Atom Count: 30,643
Modelled Residue Count: 3,605
Deposited Residue Count: 4,458
Unique protein chains: 12

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex cytochrome c subunit	A [auth O]	278	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4261 EC: 7.1.1.8
UniProt
Find proteins for A0R050 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R050 Go to UniProtKB: A0R050
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R050
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex cytochrome c subunit	B [auth M], N [auth G]	408	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4261 EC: 7.1.1.8
UniProt
Find proteins for A0R051 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R051 Go to UniProtKB: A0R051
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UniProt Group	A0R051
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex cytochrome b subunit	C [auth N], M [auth H]	556	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4263 EC: 7.1.1.8
UniProt
Find proteins for A0R052 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R052 Go to UniProtKB: A0R052
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UniProt Group	A0R052
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein	D [auth P]	100	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_2575
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QVH4 Go to UniProtKB: A0QVH4
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UniProt Group	A0QVH4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cytochrome c oxidase subunit 3	E [auth S]	203	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4260 EC: 7.1.1.9
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R049 Go to UniProtKB: A0R049
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UniProt Group	A0R049
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 4	F [auth T]	139	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4267 EC: 7.1.1.9
UniProt
Find proteins for A0R056 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R056 Go to UniProtKB: A0R056
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UniProt Group	A0R056
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	G [auth R]	575	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: D806_022970 EC: 7.1.1.9
UniProt
Find proteins for A0A2U9PNL2 (Mycolicibacterium smegmatis (strain MKD8)) Explore A0A2U9PNL2 Go to UniProtKB: A0A2U9PNL2
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UniProt Group	A0A2U9PNL2
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome-c oxidase	H [auth Q]	341	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4268 EC: 7.1.1.9
UniProt
Find proteins for A0R057 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R057 Go to UniProtKB: A0R057
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UniProt Group	A0R057
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit	I [auth U]	79	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4693
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1B6 Go to UniProtKB: A0R1B6
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UniProt Group	A0R1B6
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MSMEG_4692/MSMEI_4575	J [auth V]	157	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_4692, MSMEI_4575
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R1B5 Go to UniProtKB: A0R1B5
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UniProt Group	A0R1B5
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
LpqE protein	K [auth W]	186	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_6078
UniProt
Find proteins for A0R562 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R562 Go to UniProtKB: A0R562
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UniProt Group	A0R562
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	L [auth Y], O [auth c]	236	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: sodC, MSMEG_0835 EC: 1.15.1.1
UniProt
Find proteins for A0QQQ1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQQ1 Go to UniProtKB: A0QQQ1
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UniProt Group	A0QQQ1
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Reference Sequence

Small Molecules

Ligands 17 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IZL Query on IZL Download Ideal Coordinates CCD File SDF format, chain LB [auth G] SDF format, chain X [auth M] MOL2 format, chain LB [auth G] MOL2 format, chain X [auth M] mmCIF format, chain LB [auth G] mmCIF format, chain X [auth M]	LB [auth G], X [auth M]	[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate C₇₄ H₁₃₃ O₃₉ P RFJQNGLGKTXNKA-YXJCWACHSA-N		Interactions Focus chain LB [auth G] Focus chain X [auth M] Interactions & Density Focus chain LB [auth G] Focus chain X [auth M]
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain CA [auth N] SDF format, chain EB [auth H] SDF format, chain GA [auth P] SDF format, chain MA [auth R] SDF format, chain AA [auth N] SDF format, chain FB [auth H] SDF format, chain QA [auth R] SDF format, chain T [auth O] MOL2 format, chain BA [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain EB [auth H] MOL2 format, chain GA [auth P] MOL2 format, chain MA [auth R] MOL2 format, chain AA [auth N] MOL2 format, chain FB [auth H] MOL2 format, chain QA [auth R] MOL2 format, chain T [auth O] mmCIF format, chain BA [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain EB [auth H] mmCIF format, chain GA [auth P] mmCIF format, chain MA [auth R] mmCIF format, chain AA [auth N] mmCIF format, chain FB [auth H] mmCIF format, chain QA [auth R] mmCIF format, chain T [auth O]	AA [auth N] BA [auth N] CA [auth N] EB [auth H] FB [auth H] AA [auth N], BA [auth N], CA [auth N], EB [auth H], FB [auth H], GA [auth P], MA [auth R], QA [auth R], T [auth O]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain AA [auth N] Focus chain BA [auth N] Focus chain CA [auth N] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GA [auth P] Focus chain MA [auth R] Focus chain QA [auth R] Focus chain T [auth O] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth N] Focus chain CA [auth N] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GA [auth P] Focus chain MA [auth R] Focus chain QA [auth R] Focus chain T [auth O]
WUO Query on WUO Download Ideal Coordinates CCD File SDF format, chain HA [auth P] SDF format, chain P [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain P [auth O] mmCIF format, chain HA [auth P] mmCIF format, chain P [auth O]	HA [auth P], P [auth O]	acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2) C₇₂ H₁₃₅ O₂₄ P NUQCUWACYIKWMU-RXWIBPKHSA-N		Interactions Focus chain HA [auth P] Focus chain P [auth O] Interactions & Density Focus chain HA [auth P] Focus chain P [auth O]
9YF Query on 9YF Download Ideal Coordinates CCD File SDF format, chain V [auth M] SDF format, chain KB [auth G] SDF format, chain YA [auth W] MOL2 format, chain V [auth M] MOL2 format, chain KB [auth G] MOL2 format, chain YA [auth W] mmCIF format, chain V [auth M] mmCIF format, chain KB [auth G] mmCIF format, chain YA [auth W]	KB [auth G], V [auth M], YA [auth W]	(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate C₄₄ H₈₅ O₁₃ P GRDWPDVMAXODDM-LZYRCPELSA-N		Interactions Focus chain KB [auth G] Focus chain V [auth M] Focus chain YA [auth W] Interactions & Density Focus chain KB [auth G] Focus chain V [auth M] Focus chain YA [auth W]
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain NA [auth R] SDF format, chain OA [auth R] MOL2 format, chain NA [auth R] MOL2 format, chain OA [auth R] mmCIF format, chain NA [auth R] mmCIF format, chain OA [auth R]	NA [auth R], OA [auth R]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain NA [auth R] Focus chain OA [auth R] Interactions & Density Focus chain NA [auth R] Focus chain OA [auth R]
MQ9 (Subject of Investigation/LOI) Query on MQ9 Download Ideal Coordinates CCD File SDF format, chain HB [auth H] SDF format, chain EA [auth N] SDF format, chain FA [auth N] SDF format, chain IB [auth H] SDF format, chain S [auth O] SDF format, chain Y [auth N] MOL2 format, chain HB [auth H] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain IB [auth H] MOL2 format, chain S [auth O] MOL2 format, chain Y [auth N] mmCIF format, chain HB [auth H] mmCIF format, chain EA [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain IB [auth H] mmCIF format, chain S [auth O] mmCIF format, chain Y [auth N]	EA [auth N] FA [auth N] HB [auth H] IB [auth H] S [auth O] EA [auth N], FA [auth N], HB [auth H], IB [auth H], S [auth O], Y [auth N]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain EA [auth N] Focus chain FA [auth N] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain S [auth O] Focus chain Y [auth N] Interactions & Density Focus chain EA [auth N] Focus chain FA [auth N] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain S [auth O] Focus chain Y [auth N]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain KA [auth S] MOL2 format, chain KA [auth S] mmCIF format, chain KA [auth S]	KA [auth S]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain KA [auth S] Interactions & Density Focus chain KA [auth S]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain Q [auth O] SDF format, chain R [auth O] MOL2 format, chain Q [auth O] MOL2 format, chain R [auth O] mmCIF format, chain Q [auth O] mmCIF format, chain R [auth O]	Q [auth O], R [auth O]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain Q [auth O] Focus chain R [auth O] Interactions & Density Focus chain Q [auth O] Focus chain R [auth O]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain Z [auth N] SDF format, chain DA [auth N] SDF format, chain DB [auth H] SDF format, chain GB [auth H] MOL2 format, chain Z [auth N] MOL2 format, chain DA [auth N] MOL2 format, chain DB [auth H] MOL2 format, chain GB [auth H] mmCIF format, chain Z [auth N] mmCIF format, chain DA [auth N] mmCIF format, chain DB [auth H] mmCIF format, chain GB [auth H]	DA [auth N], DB [auth H], GB [auth H], Z [auth N]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth N] Focus chain DB [auth H] Focus chain GB [auth H] Focus chain Z [auth N] Interactions & Density Focus chain DA [auth N] Focus chain DB [auth H] Focus chain GB [auth H] Focus chain Z [auth N]
9XX Query on 9XX Download Ideal Coordinates CCD File SDF format, chain CB [auth Y] SDF format, chain PB [auth c] SDF format, chain ZA [auth W] MOL2 format, chain CB [auth Y] MOL2 format, chain PB [auth c] MOL2 format, chain ZA [auth W] mmCIF format, chain CB [auth Y] mmCIF format, chain PB [auth c] mmCIF format, chain ZA [auth W]	CB [auth Y], PB [auth c], ZA [auth W]	(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate C₃₈ H₇₄ O₄ LWLNRPPCJIGPLI-ZPGRZCPFSA-N		Interactions Focus chain CB [auth Y] Focus chain PB [auth c] Focus chain ZA [auth W] Interactions & Density Focus chain CB [auth Y] Focus chain PB [auth c] Focus chain ZA [auth W]
7PH Query on 7PH Download Ideal Coordinates CCD File SDF format, chain IA [auth S] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain W [auth M] MOL2 format, chain IA [auth S] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain W [auth M] mmCIF format, chain IA [auth S] mmCIF format, chain MB [auth G] mmCIF format, chain NB [auth G] mmCIF format, chain W [auth M]	IA [auth S], MB [auth G], NB [auth G], W [auth M]	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate C₂₉ H₅₇ O₈ P UYOIGTVMJVHOSC-HHHXNRCGSA-N		Interactions Focus chain IA [auth S] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain W [auth M] Interactions & Density Focus chain IA [auth S] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain W [auth M]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain AB [auth W] SDF format, chain BB [auth Y] SDF format, chain OB [auth c] MOL2 format, chain AB [auth W] MOL2 format, chain BB [auth Y] MOL2 format, chain OB [auth c] mmCIF format, chain AB [auth W] mmCIF format, chain BB [auth Y] mmCIF format, chain OB [auth c]	AB [auth W], BB [auth Y], OB [auth c]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AB [auth W] Focus chain BB [auth Y] Focus chain OB [auth c] Interactions & Density Focus chain AB [auth W] Focus chain BB [auth Y] Focus chain OB [auth c]
TRD Query on TRD Download Ideal Coordinates CCD File SDF format, chain JA [auth S] SDF format, chain LA [auth T] SDF format, chain SA [auth R] SDF format, chain TA [auth R] SDF format, chain XA [auth Q] MOL2 format, chain JA [auth S] MOL2 format, chain LA [auth T] MOL2 format, chain SA [auth R] MOL2 format, chain TA [auth R] MOL2 format, chain XA [auth Q] mmCIF format, chain JA [auth S] mmCIF format, chain LA [auth T] mmCIF format, chain SA [auth R] mmCIF format, chain TA [auth R] mmCIF format, chain XA [auth Q]	JA [auth S], LA [auth T], SA [auth R], TA [auth R], XA [auth Q]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain JA [auth S] Focus chain LA [auth T] Focus chain SA [auth R] Focus chain TA [auth R] Focus chain XA [auth Q] Interactions & Density Focus chain JA [auth S] Focus chain LA [auth T] Focus chain SA [auth R] Focus chain TA [auth R] Focus chain XA [auth Q]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain JB [auth G] SDF format, chain U [auth M] MOL2 format, chain JB [auth G] MOL2 format, chain U [auth M] mmCIF format, chain JB [auth G] mmCIF format, chain U [auth M]	JB [auth G], U [auth M]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain JB [auth G] Focus chain U [auth M] Interactions & Density Focus chain JB [auth G] Focus chain U [auth M]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain PA [auth R] SDF format, chain VA [auth Q] SDF format, chain WA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain VA [auth Q] MOL2 format, chain WA [auth Q] mmCIF format, chain PA [auth R] mmCIF format, chain VA [auth Q] mmCIF format, chain WA [auth Q]	PA [auth R], VA [auth Q], WA [auth Q]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain PA [auth R] Focus chain VA [auth Q] Focus chain WA [auth Q] Interactions & Density Focus chain PA [auth R] Focus chain VA [auth Q] Focus chain WA [auth Q]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain RA [auth R] MOL2 format, chain RA [auth R] mmCIF format, chain RA [auth R]	RA [auth R]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain RA [auth R] Interactions & Density Focus chain RA [auth R]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain UA [auth R] MOL2 format, chain UA [auth R] mmCIF format, chain UA [auth R]	UA [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain UA [auth R] Interactions & Density Focus chain UA [auth R]